[gmx-users] Area per lipid calculation

NG HUI WEN HuiWen.Ng at nottingham.edu.my
Fri Nov 19 01:09:22 CET 2010

Dear gromacs users, 


I have a protein embedded in a lipid bilayer. After sufficient
equilibration of the system ( i.e. size of box X and Box Y became quite
constant), I would now like to assess the area per lipid of my system. 


However, (I think) I could not simply do this  ( average size of box X *
average size of box Y/ number of lipids per monolayer) because there is
a protein in the middle of the bilayer. Ideally I would first like to
calculate the area occupied by the protein then take the difference
between the two as my answer. I notice this is how the inflategro script
calculates the estimated area per lipid during the shrinking process.  


I have had a search through the mailing list to look for an answer but
to no avail. It seems I might need a script to perform that? 


Thank you for your help.



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